lecture 5.105 Amino acids

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 3 This imparts some important properties to proteins, which we will see later. Since amino acids all have the  amino and carboxyl groups, the peptide bond can, in principle, be formed in either direction. This is why proteins are linear polymers of amino acids joined by peptide bonds. Recall the general structure of an amino acid in the neutral pH form: Proteins are made from 20 different L-amino acids. The amino acids can be grouped together in many different ways, and we'll go through the using the grouping from Lehninger. In order to facilitate writing them down, amino acids have been given abbreviations. There are individual three-letter and one-letter abbreviations, which you must learn. For instance, Glycine is abbreviated Gly or G. Not always easy. For instance, Glutamine is abbreviated Gln or Q. I will give you the long, three letter abbrev and the one letter abbrev. I will also give you a number that corresponds to the hydrophobicity of the amino acid. There are a couple of scales that can be used, and I’ll just pick one. In this scale, plus = hydrophobic and negative = hydrophilic. Scale goes from +4.5 (Ile) to -4.5 (Arg). Think of it as related to the change in Gibbs free energy in moving the amino acid from non-polar solvent (acetone) to water. Draw bar to the far right. GROUP 1; NON-POLAR, ALIPHATIC (OFTEN HYDROPHOBIC) G,A,V,L,I,P

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 6 Glutamine, Gln, Q , -3.5 Similar properties as Asn GROUP 3; AROMATIC F,Y,W Phenylalanine; Phe, F , 2.8 V. hydrophobic. Large and bulky. Strong UV absorber; more on this in a minute. Tyrosine; Tyr, Y , -1.3 V. active side group. Strong H-bonder. Acid/base properties, pK a = 10.1. pK a beyond physiol pH range. Tryptophan; Trp, W , -0.9 Largest amino acid; rarest. Heterocyclic. Does not deprotonate, but does H-bond. Beer's Law - Relating Absorbance to Concentration A technique used very often in the lab is to measure the absorbance of a compound at a particular wavelength, and then to use that to calculate the compound's concentration. A = -log(I out /I in ) Put in wavelength; A  = log(I  (in) /I  (out) ) Beer's Law; A  =    c  d Definitions: (Put on different place on board that can be saved)  = wavelength I in , I out = light intensity going in, coming out. A  = absorbance at  c = concentration in whatever units d = distance across the light path; usually = 1 cm   = extinction coefficient; units of conc -1  dist -1

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 9 I will show you how to work a couple of problems concerning the acid/base properties of amino acids. 1. What is the pH of 0.1 M monosodium glutamate? Ans: What are the different types of glutamate? What are the charges? Start with the most acidic form The name tells you that there is one Na + balancing a - charge in glutamate. So you are starting with the third species from the left. Since this compound is amphoteric, pH = ½ (pK a2 + pK a3 ) = ½ (4.2 + 9.7) = 6.95 2. What is the pH of isoelectric glutamic acid? Ans: Start with the uncharged form, second from the left. pH = ½ (2.2 + 4.2) = 3.2

Biological Sciences 105 Lecture 5, October 1, 2018 Copyright Steven M. Theg, 2087. All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 12 When a peptide bond is formed, the Ns and Cs involved are no longer available for titration. So they drop out of the problem. Only the N-terminus of G, the C-terminus of A and the  -amine of K are part of the charge/pH calculation. Write the peptide from N to C terminus, and then from most acidic on left to most basic on right. Look at the charge on the different species. Define pI as the isoelectric point, the pH at which there is no charge. This applies to peptides as well as AAs. The sequence of amino acids in a protein is called the protein’s primary structure. This forms the backbone of the protein. It is always written N-terminus to C-terminus. SOME EQUATIONS YOU’VE HAD THAT YOU SHOULD MEMORIZE ΔG = ΔH - TΔS ΔG°’ = - RTlnKeq ΔG = ΔG°’ + RTln{[products]/[reactants]} pH = pKa + log{[A-]/[HA]} Please do the practice problems.